Due to EMC problems on our board, which is similar to the Evaluation Kit of the AT91SAM9263 it is necessary to change the clock at runtime.

Based on the "at91_slow_clock" routine (pm_slowclock.S) which is used in power safe mode, we implemented a function which is executed in sram and changes the plla register.

But as soon the plla register is changed, the system reboots.
(When writing the same value as in the initialisation process, it works).

Any ideas, what we missed?

>>Any ideas, what we missed?

Absent the code you're using, I'd guess that you are trying to change the clock you're actually using, rather than switching to a different one (ie not CLKA), and waiting for the PLL/VCO to attain lock, before switching back.